Sequence Diagrams are some kind of special in Enterprise Architect.
When adding a message to a Sequence Diagram Enterprise Architect recalculates the other Messages and changes properties like SeqNo, Offsets, ... .
When working parallel on the same Sequence Diagram in different branches, adding/removing messages and merging them with LemonTree may cause unexpected results with positioning of the messages since LemonTree is a compare/merge tool and does not recalculate the diagram as EA does when adding a message to the Sequence diagram.
An example is always good for understanding (especially in this case):
In this example we have a simple Sequence Diagram with only a few connectors. We change the Sequence Diagrams in both branches "A" and "B"
When experiencing such a case LemonTree shows a conflict and it's worth taking a look in the written merge file at the conflicted Sequence Diagram. Messages are maybe dislocated and also are no longer in the fragments they belong to.
Note: The diagram may also look different in Enterprise Architect than in LemonTree Merge Preview because Enterprise Architect draws it different. The new connectors are NOT on the same level.